Protocol for genomic mapping of chromatin targets using high-throughput CUT&RUN

The genomic distribution of proteins that define chromatin state, including transcription factors, chromatin modifiers, and histone modifications, is critical for understanding gene regulation, cellular identity, and disease development. Here, we present a high-throughput cleavage under targets and release using nuclease (CUT&RUN) protocol performed in 96-well plate format. We describe steps for targeted DNA enrichment, high-quality library preparation, sequencing, and data analysis. This protocol enables high-resolution genomic mapping of proteins of interest and factors that define the epigenome. For complete details on the use and execution of this protocol, please refer to Skene and Henikoff¹ and Meers et al.².